Some other options for helping larger missiles be more viable are:
Increased damage efficiency as your warhead gets larger. After all, you just need one fuze regardless of warhead size. Thus if a 2.0 MSP warhead was more than twice as strong than a 1.0 MSP warhead, you'd be making an actual trade off of Damage vs Chance of a Hit.
Either a new armor tech could be added, properties could be added to existing armor or a new module could be added that grants minor damage resistance. This kind of already exists with shields, if you can't do damage faster than it recharges, you're in trouble. Something similar to Sword of the Stars 2's damage resistance could be added to armor that would negate some of the damage pattern of weapons. For example, if a missile did damage in a 5-3-1 pattern (top to bottom), one level of resistance would negate the highest row leaving 3-1. Or maybe just the lowest level leaving 5-3. Either way, unless a size 1 missile happened to hit a section of armor that had been completely destroyed, it would be ineffective. Like throwing a grenade against a tank vs throwing the same grenade inside an open hatch. Ideally this would greatly increase the mass of armor, so that smaller frigates and destroyers might shrug off AMMs, but only much larger heavily armored warships could afford to protect against larger missiles.
Having distance based accuracy penalties that can be countered by adding small amounts of MSPs in the form of onboard AIs or better communication gear. Since any missile with no onboard sensor is reliant on the firing ship's MFC, this can be explained as the missile relying less on the firing ship to provide instructions that may be experiencing a delay due to the distance from the firing ship. This would limit AMMs to a much shorter range, while larger missiles can devote some space to maintaining their accuracy at a longer ranger. Then again, I can't remember of Aurora is supposed to have FTL communication cananocially or not. If it does, it renders this on pointless.
Finally, building upon the last one, giving missile fire control's a limit to the number of active missiles they can control at a time. If your currently designed MFC can only control six missiles in flight at once, you'll probably want larger missiles that can attack from further out. Otherwise a beam armed ship might be able to realistically close the range without taking critical damage. New tech can influence the number of missiles controllable per launcher. Ideally your fire control links would be pooled together based on range, so if you had two AMM MFCs that can control 6 missiles at 60M KM each, and two ASM MFCs that can control 3 missiles at 300M KM, you attack with six missiles at a time, or the two ASM MFCs could be handed control of six AMMs to increase the density of your defensive fire. (Or likewise increase your offensive fire once you got within 60M KM).